tbuckley/cabot-search huggingface dataset:
Abstract 5373: Autoencoder-based multimodal prediction of survival for non-small cell lung cancer
Authors: Jacob G. Ellen, Etai Jacob, Nikos Nikolaou, Natasha Markuzon
Journal: Cancer Research (2023)

Abstract Most non-small cell lung cancer (NSCLC) prognosis prediction approaches use one data type and do not take advantage of the large amount of multimodal data available. To evaluate and explore the benefits of multimodal data integration, we present a combined feature selection and denoising autoencoder pipeline for NSCLC survival prediction and survival subtype identification using microRNA (miRNA), mRNA, DNA methylation, long non-coding RNA (lncRNA) and clinical data. Survival performance for both lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) patients was compared across modality combinations, data integration time and training data types. Multimodal data combinations outperformed single data modalities, with the early integration of all data modalities achieving concordance indexes (C-indexes) of 0.67 (±.04) and 0.63 (±.02) for LUAD and LUSC, respectively versus corresponding C-index of 0.64 (±.02) and 0.59 (±.03) for the best single cell modality (clinical). Notably, combining just lncRNA and clinical data facilitated effective survival discrimination, with C-indexes of 0.69 (±.03) for LUAD and 0.62 (±.03) for LUSC. Overall, higher performance was achieved by using a single denoising autoencoder for all biological data (early integration) and by training on both LUSC and LUAD patient data together. Two survival subtypes (log rank test p-value=1e-9) were identified, with 991 differentially expressed transcripts in the poorer survival group. Our analysis shows the value of multimodal data integration for predicting NSCLC progression, with especially good performance using the combination of lncRNA and clinical data. Early integration of biological data, with an initial linear feature selection technique and a denoising autoencoder for dimensionality reduction, showed effective survival performance and survival subtype identification. Further research is underway to expand analysis to different cancer types and data modalities and extract more biological interpretability from autoencoder models. Citation Format: Jacob G. Ellen, Etai Jacob, Nikos Nikolaou, Natasha Markuzon. Autoencoder-based multimodal prediction of survival for non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5373.
Abstract 1446: The elevated expression of INSM1 is correlated with EZH2 in neuroendocrine prostate cancer
Authors: Lin Li, Siyuan Cheng, Xiuping Yu
Journal: Cancer Research (2023)

Abstract Background: Neuroendocrine prostate cancer (NEPCa) is the most aggressive and non-targetable prostate cancer (PCa). It is well accepted that NEPCa arises from prostate adenocarcinoma (AdPCa) via trans-differentiation. NEPCa tumors exhibit a similar mutation burden but a different transcriptome profile from AdPCa. This suggests that the acquisition of the NE phenotype is driven by epigenetic, transcriptional reprogramming but not genetic alterations. Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, is an epigenetic regulator and upregulated in NEPCa. The upregulation of EZH2 in PCa has been considered to be correlated with therapy-induced plasticity and NE differentiation. Insulinoma-associated 1 (INSM1), is a zinc-finger transcription factor, which is predominantly expressed in neuroendocrine (NE) cells and important for the NE developmental pathways. INSM1 has been considered as a biomarker for multiple types of NE tumors, like pancreatic, lung, and prostate. Also, the increase level of INSM1 is associated with NE differentiation in PCa. Analysis of PCa transcriptomic profiles suggests that EZH2 and INSM1 have positive correlation in PCa and function together in NEPCa. Methods: To study the expression of INSM1 and EZH2, we did immunofluorescence (IF), immunohistochemistry (IHC), Western blot and RT-qPCR in prostate cancer cell lines, mouse tissues, and human patients samples. The bioinformatics analysis was done using the publicly available RNA-Seq data obtained from the cBioportal, the Cancer Genome Atlas (TCGA), and the Cancer Cell Line Encyclopedia websites (CCLE). Results and Conclusion: Our IHC results confirmed that INSM1 is highly expressed in NEPCa rather that AdPCa in both human and mouse tissues. By IF, we further found that INSM1 also expresses in PCa amphicrine cells. Additionally, we found that the expression of INSM1 is positively associated with EZH2 expression in PCa. These data indicates that INSM1 may act as a marker for not only NE cells but also amphicrine cells in PCa. Also the correlation between INSM1 and EZH2 further indicates the importance of INSM1 in NEPCa. Our further study will focus on how INSM1 functions and whether there’s a direct regulation between INSM1 and EZH2. Acknowledgement: This work was supported by NIH R01 CA226285, and the Feist-Weiller Cancer Center (FWCC). Citation Format: Lin Li, Siyuan Cheng, Xiuping Yu. The elevated expression of INSM1 is correlated with EZH2 in neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1446.
Abstract 3465: HDAC8 regulates immune escape in melanoma through increased transcription of inhibitory cytokines that increase accumulation of myeloid-derived suppressor cells (MDSCs)
Authors: Chao Zhang, Michael Emmons, Richard Bennett, Jonathan Licht, Keiran Smalley
Journal: Cancer Research (2023)

Abstract Immune checkpoint blockade leads to improved and durable responses in 30-40% of melanoma, yet nearly 1/3 of patients relapse from complete remission within 3 years. Recent studies from our group and others demonstrated that upfront use of targeted therapy leads to decreased immune infiltrate and confers resistance to immunotherapy. We have previously showed that HDAC8 reprograming cell transcriptional states leads to reduced recognition by immune system. However, it’s unclear how HDAC8 activity modulates the tumor immune microenvironment (TIME). In this study, we used integrated single cell RNA-seq, ATAC-seq and a novel BRAF-V600E; PTEN+/- melanoma genetically engineered mouse model (GEMM) to explore “cold” TIME modulated by HDAC8. Analysis of human melanoma cells overexpressing HDAC8 by ATAC-seq, ChIP-Seq and RNA-Seq showed that HDAC8 expression significantly increases chromatin accessibility, H3K27 promoter region acetylation and gene expression of IL-11. Increased IL-11 protein expression was confirmed by cytokine array in isogenic SM1 mouse melanoma cells expressing HDAC8.Overexpression of HDAC8 in the GEMM accelerated melanoma development and was associated with worse overall survival rate. Analysis of HDAC8 and control tumors by scRNA-seq and immunohistochemistry (IHC) showed that HDAC8 overexpressing tumors dramatically decreased CD4 and CD8 T cell infiltration and increased MDSCs and IL-11 expression. We next explored whether IL-11 drives the expansion and polarization of MDSCs and subsequent reduction in T cell infiltration and activation. A MDSCs polarization assay demonstrated that addition of IL-11 led to increased expansion and polarization of MDSCs from mouse bone marrow myeloid cells. A MDSCs suppression assay confirmed IL-11 induced MDSCs accumulation significantly reduced T cell proliferation and activation. We show for the first time that HDAC8 expression regulates immune escape by activating IL-11 expression and driving MDSCs expansion. Going forward, inhibition of HDAC8 activity is intriguing as a novel therapeutic strategy to reverse tumor derived immune suppression and to ultimately improve patient responses to immunotherapy. Citation Format: Chao Zhang, Michael Emmons, Richard Bennett, Jonathan Licht, Keiran Smalley. HDAC8 regulates immune escape in melanoma through increased transcription of inhibitory cytokines that increase accumulation of myeloid-derived suppressor cells (MDSCs) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3465.
Abstract 4478: Up284, A small molecule inhibitor of ADRM1 demonstrates significant anti-tumor efficacy in preclinical models of aggressive breast cancer
Authors: Balasubramanyam Karanam, Ravi Anchoori, Yung-Nien Chang, Rachel Martini, Florencia Madorsky Rowdo, Melissa B. Davis
Journal: Cancer Research (2023)

Abstract Quadruple-negative breast cancer (QNBCs) is a highly aggressive and metastatic disease and remains clinically challenging breast cancer subtype with worst prognosis. Due to its exceeding heterogeneity, absence of the AR, ER, PR, Her2 receptors and lack of established therapeutic targets, QNBC is hard to treat cancer and recurs rapidly with standard chemo regimen. QNBC demonstrated vulnerability to proteasome inhibition due to their higher metabolic needs. But FDA approved 20S proteasome inhibitors failed to treat solid tumors including QNBC. Hence, developing an effective strategy to overcome the limitations associated with current 20S proteasome inhibitors is mandated to provide alternate treatment options for QNBC patients. Preclinical, Up Therapeutics lead candidate small molecule inhibitor Up284 has shown significant tumor growth inhibition as a single agent in animal models. To explore potential synergy of Up284 with other therapeutic agents, we conducted the in vivo combination experiments. In this work, we present ADRM1 amplification in QNBC tumors, identification of a small molecule selective inhibitor of ADRM1, Up284 (Up Therapeutics), Up284 demonstrated efficacy against panel of BC cell lines and patient derived organoids. In vivo combination results for Up284 with widely used BC standard-of care chemotherapy regimen demonstrated strong in vivo synergy in tumor mouse syngeneic models. Taken together, these data demonstrated combination synergy of a small molecule ADRM1 inhibitor with other agents. These results pave the road for potential clinical evaluation of combination treatment of QNBC in patients. Citation Format: Balasubramanyam Karanam, Ravi Anchoori, Yung-Nien Chang, Rachel Martini, Florencia Madorsky Rowdo, Melissa B. Davis. Up284, A small molecule inhibitor of ADRM1 demonstrates significant anti-tumor efficacy in preclinical models of aggressive breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4478.
Abstract 2757: Combination of a fluorescent substrate-based MMP activity assay and hit pick reading/imaging procedure to screen for inhibitors of MT1-MMP activity and 3D glioma tumoroid invasion
Authors: Brad Larson, Gregg Fields, Ania Knapinska
Journal: Cancer Research (2023)

Abstract Malignant and nonmalignant brain tumors are composed of a group of more than 100 different types. Malignant gliomas, including glioblastoma multiforme (GBM) and astrocytomas, are the most common primary brain tumors in the United States, and make up 78% of malignant brain tumors. Membrane type 1 matrix metalloproteinase (MT1-MMP) has been shown to be crucial for the progression, invasion, migration, and angiogenesis of tumors. Use of a FRET substrate to quantify MT1-MMP activity, where tumoroids are embedded in a collagen hydrogel, would simplify detection of potential protease inhibitors, while using an in vivo-like cell model. In the present study, multiple glioma cell lines were formed into tumor spheroids, followed by type I collagen addition. Many known MT1-MMP inhibitors were then added to the wells, to potentially inhibit invasion of the 3D cell models. The substrate and experimental setup were then combined with the joint reading and imaging process available in the Agilent BioTek Gen5 microplate reader and imager software, to create a hit pick screening method. During the procedure, all control and test wells were read, and the signal from cleaved substrate was quantified. Uninhibited invasion within positive control wells exhibited high fluorescence values. Therefore, a hit pick criterion was established such that any wells containing test molecules that were statistically lower than average in fluorescent signal from the corresponding positive control, which should exhibit inhibited invasion, were imaged. Wells that were not significantly lower were not imaged. The result was a screening method which increased efficiency by reducing image capture time and storage requirements. Citation Format: Brad Larson, Gregg Fields, Ania Knapinska. Combination of a fluorescent substrate-based MMP activity assay and hit pick reading/imaging procedure to screen for inhibitors of MT1-MMP activity and 3D glioma tumoroid invasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2757.
Abstract 3466: Microbial neoantigen vectors for cancer immunotherapy
Authors: Andrew A. Redenti, Tal Danino, Nicholas Arpaia
Journal: Cancer Research (2023)

Abstract Cancers employ a variety of immunosuppressive and evasive mechanisms to avoid detection by the immune system and prevent tumor neoantigen-mediated elimination. In recent years, tumor-specific neoantigen vaccines have shown significant promise—promoting tumor regression and increasing survival benefit in certain malignancies by therapeutically directing the immune system to target previously protected tumor specific antigens. However, despite encouraging preclinical data, objective and durable responses have remained elusive—highlighting a requirement for improved therapeutic platforms that permit delivery and targeting of diverse sets of tumor antigens to enhance the efficacy of cancer vaccines. Through synthetic biology, we have engineered living microbial vectors harboring constructs encoding synthetic arrays of tumor-specific neoantigens that specifically colonize tumors following intravenous injection and deliver high levels of neoantigen cargo—both extracellularly (within the tumor microenvironment) and intracellularly (to the cytosol of tumor-resident phagocytes). These engineered vectors robustly activate innate immune cascades and effectively prime tumor neoantigen-directed T cell responses to promote tumor regression and survival in advanced murine solid tumor and lung metastasis models. Extensive remodeling of the tumor immune microenvironment accompanies therapeutic efficacy, with increased activation of tumor neoantigen-specific CD4+ and CD8+ T cells, broadened stimulation of tumor-infiltrating B and T cells, and reduced numbers of intratumoral myeloid cells exhibiting immunosuppressive phenotypes. This work provides a foundational platform for the development of a new class of next-generation tumor vaccines, leveraging the advantages of living medicines to deliver diverse arrays of tumor-specific neoantigens within the optimal immunostimulatory context to induce potent anti-tumor immunity. Citation Format: Andrew A. Redenti, Tal Danino, Nicholas Arpaia. Microbial neoantigen vectors for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3466.
Abstract 284: Sigma1 regulates lipid droplet mediated redox homeostasis required for prostate cancer proliferation
Authors: Halley M. Oyer, Alexandra R. Steck, Charles Longen, Sanjana Venkat, Konuralp Bayrak, Eleanor Munger, Dan Fu, Christina Sanders, Justin Myers, Matthew Schiewer, Nan Chen, Elahe Mostaghel, Felix J. Kim
Journal: Cancer Research (2023)

Abstract Lipid droplets (LDs) are dynamic organelles that serve as hubs of cellular metabolic processes. Emerging evidence shows that LDs also play a critical role in maintaining redox homeostasis and can mitigate lipid oxidative stress. In multiple cancers, including prostate cancer (PCa), LD accumulation is associated with cancer aggressiveness, therapy resistance, and poor clinical outcome. PCa arises as an androgen receptor (AR) driven disease. Among its myriad roles, AR mediates the biosynthesis of LDs, induces autophagy, and modulates cellular oxidative stress in a tightly regulated cycle that promotes cell proliferation. The factors regulating the interplay of these metabolic processes downstream of AR remain unclear. Here, we show that Sigma1/SIGMAR1, a unique ligand-operated scaffolding protein, regulates LD metabolism in PCa cells. Sigma1 inhibition triggers lipophagy, an LD selective form of autophagy, to prevent accumulation of LDs which normally act to sequester toxic levels of reactive oxygen species (ROS). This disrupts the interplay between LDs, autophagy, buffering of oxidative stress and redox homeostasis, and results in the suppression of cell proliferation in vitro and tumor growth in vivo. Consistent with these experimental results, SIGMAR1 transcripts are strongly associated with lipid metabolism and reactive oxygen species pathways in prostate tumors. Altogether, these data reveal a novel, pharmacologically responsive role for Sigma1 in regulating the redox homeostasis required by oncogenic metabolic programs that drive PCa proliferation. Citation Format: Halley M. Oyer, Alexandra R. Steck, Charles Longen, Sanjana Venkat, Konuralp Bayrak, Eleanor Munger, Dan Fu, Christina Sanders, Justin Myers, Matthew Schiewer, Nan Chen, Elahe Mostaghel, Felix J. Kim. Sigma1 regulates lipid droplet mediated redox homeostasis required for prostate cancer proliferation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 284.
Abstract 2755: Identification of novel GPX4 inhibitors using global transcriptional reporters
Authors: Timothy Read, Zoe Winigrad, Ardeshir Goliaei, Cole Liechty, Carter Grochala, Leah Damon, John Dickson, Jason Harris, Casey Pham, Jenna Rimel, Christy Rhine, Dave Simpson, Eric Martin, Joey Azofeifa
Journal: Cancer Research (2023)

Abstract Induction of Ferroptosis is a promising strategy for treating therapy-resistant tumors including mesenchymal tumor types. We performed a phenotypic screen to identify small molecules that induce ferroptosis in mesenchymal cancer cells by screening for compounds whose toxicity could be rescued by the lipophilic antioxidant Ferrostatin-1. To identify compounds that induce GPX4-mediated ferroptosis, we identified several pharmacodynamic biomarkers specific to GPX4 inhibition using our nascent RNA sequencing platform, which allows for time-resolved snapshots of global transcription. We measured the transcriptional changes that occur in the hours following inhibition of GPX4 and identified HMOX1 as a robust biomarker of GPX4i-induced ferroptosis in mesenchymal cancer cell lines. Using HMOX1-induction as a guide, we uncovered a small number of compounds as potential GPX4 inhibitors. One such compound was validated as a bonafide GPX4 inhibitor through a variety of biochemical assays and selected for a hit-to-lead campaign. In addition to standard medicinal chemistry strategies, we are currently employing a newly-developed global transcriptional reporter system to stratify several novel series of GPX4 inhibitors by their transcriptional signatures. This approach represents a unique strategy for determining on- and off- target effects of a compound and for defining structure activity relationships within a chemical series. Citation Format: Timothy Read, Zoe Winigrad, Ardeshir Goliaei, Cole Liechty, Carter Grochala, Leah Damon, John Dickson, Jason Harris, Casey Pham, Jenna Rimel, Christy Rhine, Dave Simpson, Eric Martin, Joey Azofeifa. Identification of novel GPX4 inhibitors using global transcriptional reporters [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2755.
Abstract 674: CRISPR and drug screens identify ERK as the mediator of IFNg-induced melanoma growth inhibition
Authors: Ameya S. Champhekar, Rachel Heymans, Cynthia Gonzalez, Guillem Turon Font, Daniel Karin, June Lee, Robert Damoiseaux, Antoni Ribas
Journal: Cancer Research (2023)

Abstract Interferon-gamma (IFNg) is critical for the success of immune checkpoint blockade therapy. Disruption of IFNg signaling makes tumors resistant to anti-PD-1/L1 treatment primarily by evasion of the growth inhibition (GI) induced by this cytokine. However, the pathways mediating IFNg-induced GI are largely unknown. We used two independent approaches to delineate the IFNg GI pathway, a chemical genomics screen and a whole genome targeting CRISPR/Cas9 screen in an IFNg GI-sensitive patient-derived melanoma (PDM) cell line. Drug screening revealed that treatment with RAF and ERK inhibitors disrupted IFNg GI in PDM cells. For the CRISPR screen, gene-level analysis showed that the magnitude of enrichment for guide RNAs targeting ERK2 in IFNg-treated cells was comparable to proximal IFNg signaling proteins like JAK1, STAT1, IFNGR2, and JAK2 (&amp;gt;26-fold enrichment for ERK2, p = 2.28e-07). Thus, results from both these experiments converged upon ERK as the primary downstream target of IFNg essential for GI induction. We validated the involvement of ERK by detecting a sustained increase in phospho-ERK1/2 levels following IFNg treatment. In live imaging experiments, we found that blocking ERK activity with the ERK inhibitor Ulixertinib blocks the induction of cell death after IFNg treatment in 17 of 23 (~74%) IFNg-sensitive PDM lines covering all the MAPK mutant and triple wildtype molecular subtypes of melanoma. Decreasing and increasing ERK activity levels using shRNA and overexpression approaches also led to a decrease and increase in IFNg-mediated GI, respectively. We have identified NOXA and DR5 as likely mediators of cell death through the IFNg-ERK GI pathway by comparing gene expression profiles of control and IFNg-treated PDM cells. Finally, phorbol 12-myristate 13-acetate (PMA), a known ERK activator, synergizes with IFNg treatment to induce increased GI in PDM cells (Bliss synergy score 16.87, p = 1.83e-123). In summary, the IFNg-ERK signaling axis mediates cell death downstream of IFNg treatment in melanoma cells. This pathway is active in all melanoma subtypes, making it an attractive target to enhance IFNg GI in tumor cells. Our results provide a new understanding of the IFNg GI pathway that will also be crucial to define mechanisms of GI resistance in tumor cells. Citation Format: Ameya S. Champhekar, Rachel Heymans, Cynthia Gonzalez, Guillem Turon Font, Daniel Karin, June Lee, Robert Damoiseaux, Antoni Ribas. CRISPR and drug screens identify ERK as the mediator of IFNg-induced melanoma growth inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 674.